sorry, forgot to respond earlier. Which V1 label are you using? You might
try thresholding it to remove the low-probability vertices that make it
larger than it should be
cheers
Bruce
On Mon, 11 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels drawn in fsaverage to
subject’s space (using mri_label2label).
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left
and right hemisphere that I want to convert to a subjects brain. I’ve
successfully managed to do this for the left hemisphere of all the subjects,
where the V1-bins converted from the fsaverage fall perfectly within subject
specific V1. However, for the right hemisphere, the bins seem slightly
misaligned for all the subjects (they’re usually a bit bigger than they
should be). Any idea what could have caused this?!
Attached the image that shows the fine conversion for the lh (on the left)
and the misaligned conversion for the rh (on the right)
[IMAGE]
I used the following commands:
left hemisphere, first bin:
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface
right hemisphere
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface
The output is as follows:
left hemisphere, first bin:
srclabel = ./fsaverage/label/lh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = HHcon_8
trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 102 points in source label.
Starting surface-based mapping
Reading source registration
/Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/Applications/freesurfer/subjects/HHcon_8/surf/lh.white
Reading target registration
/Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 102 nlabel points
Performing mapping from target back to the source label 118606
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132
mri_label2label: Done
right hemisphere, first bin:
srclabel = ./fsaverage/label/rh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = con21_oxford
trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 209 points in source label.
Starting surface-based mapping
Reading source registration
/Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/Applications/freesurfer/subjects/con21_oxford/surf/rh.white
Reading target registration
/Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg
Rescaling ... original radius = 99.9999
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 209 nlabel points
Performing mapping from target back to the source label 145838
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294
mri_label2label: Done
So for some reason the conversion for the right hemisphere works but is not
perfect, which is also reflected in the fact that extracting the label
statistics (using mris_anatomical_stats) will sometimes give different
values after re-running the conversion.
Hinke N. Halbertsma, MSc
PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl
On 01 Jul 2016, at 16:11, Halbertsma, HN (ohk)
<h.n.halbert...@umcg.nl> wrote:
Hi Bruce,
Attached the image that show the fine conversion for the lh (on the
left) and the misaligned conversion for the rh (on the right)
<mri_label2label_leftright.jpg>
I used the following commands:
left hemisphere, first bin:
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod
surface
right hemisphere
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod
surface
The output is as follows:
left hemisphere, first bin:
srclabel = ./fsaverage/label/lh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = HHcon_8
trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 102 points in source label.
Starting surface-based mapping
Reading source registration
/Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/Applications/freesurfer/subjects/HHcon_8/surf/lh.white
Reading target registration
/Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 102 nlabel points
Performing mapping from target back to the source label 118606
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132
mri_label2label: Done
right hemisphere, first bin:
srclabel = ./fsaverage/label/rh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = con21_oxford
trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 209 points in source label.
Starting surface-based mapping
Reading source registration
/Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/Applications/freesurfer/subjects/con21_oxford/surf/rh.white
Reading target registration
/Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg
Rescaling ... original radius = 99.9999
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 209 nlabel points
Performing mapping from target back to the source label 145838
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294
mri_label2label: Done
So for some reason the conversion for the right hemisphere works but
is not perfect, which is also reflected in the fact that extracting
the label statistics (using mris_anatomical_stats) will sometimes give
different values after re-running the conversion.
Hope this helps.
Hinke N. Halbertsma, MSc
PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room
124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl
On 01 Jul 2016, at 15:40, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Hinke
we need more details if you want us to help you. Images, exact
command lines and outputs, etc....
cheers
Bruce
On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels
drawn in fsaverage to
subject’s space (using mri_label2label).
I’ve manually drawn labels (V1-bins) in the
fsaverage brain in both the left
and right hemisphere that I want to convert to a
subjects brain. I’ve
successfully managed to do this for the left
hemisphere of all the subjects,
where the V1-bins converted from the fsaverage fall
perfectly within subject
specific V1. However, for the right hemisphere, the
bins seem slightly
misaligned for all the subjects (they’re usually a
bit bigger than they
should be). Any idea what could have caused this?!
Many thanks.
Hinke
Hinke N. Halbertsma, MSc
PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2, 9713
AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl
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